Is there a way to only store keyframes of only selected bones in poseLib?
pose library won't save positions of bones with DEF in the beginning of their name. You could try that for a basic ignoring of specific bones.

Or to disable bones in a keyframes 
From:
https://www.blender.org/forum/viewtopic.php?p=107151&amp;sid=ad277a6cd901c3e716346e1bdd51c371#p107151
"Mute the Bone's animation channels in F-Curve Editor and change frame to update 3d view:"

The only other way I can think of is to use a script which grabs all of the keyframes and allows you to modify only parts of that script before being run again.

I suggest you look into scripting and start with some of the codes here: How to get keyframe data from python?